screen_bam_eff: An efficient function to identify sites of interestes from a...

In sdwfrost/popseq: Population Analysis of Deep Sequencing Data

Description

An efficient function to identify sites of interestes from a list of longitudinal sequence file.

Usage

screen_bam_eff(file_list, ref = NULL, region, priorPA = 0.001)

Arguments

file_list	A list of bam files.
ref	A referece sequence.
region	An optional region from the BAM file (as a GRanges object)
priorPA	Prior assocation to possible models

Value

PPA association for each site.

Author(s)

Fei Xiang ([e-mail])

Examples

p4305.d3=system.file("extdata/4305-d3.bam",package = "popseq")
p4305.d4=system.file("extdata/4305-d4.bam",package = "popseq")
p4305.d5=system.file("extdata/4305-d5.bam",package = "popseq")
ref=system.file("extdata/A_England_195_2009.fa",package = "popseq")



pigbam=list(p4305.d3,p4305.d4,p4305.d5)


res1=screen_bam_eff(file_list=pigbam,ref=ref,region= GRanges("GQ166656_1",IRanges(1,2280)),priorPA=.001)

res2=screen_bam_eff(file_list=pigbam,ref=ref,region = GRanges("GQ166655_2",IRanges(1,2274)),priorPA=.001)

sdwfrost/popseq documentation built on May 29, 2019, 4:23 p.m.